Variant report

Variant	rs501250
Chromosome Location	chr5:112155793-112155794
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:112155496-112155820	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112152202..112156283-chr5:112195630..112198484,4	MCF-7	breast:

Variant related genes	Relation type
APC	TF binding region
ENSG00000272869	Chromatin interaction
ENSG00000153037	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10463643	0.97[GIH][hapmap]
rs1069061	0.85[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap]
rs1093611	0.84[CEU][hapmap];0.80[TSI][hapmap]
rs1093677	0.87[GIH][hapmap]
rs12656359	0.81[AFR][1000 genomes]
rs1441375	0.84[CEU][hapmap]
rs153548	0.84[CEU][hapmap]
rs1661035	0.88[CEU][hapmap]
rs1734243	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1816769	0.86[CHB][hapmap]
rs187075	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1966477	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2431238	1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs2431240	0.83[AFR][1000 genomes]
rs2431242	0.83[ASN][1000 genomes]
rs2439591	0.85[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2464805	0.85[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2545159	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2545162	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2545163	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2545164	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2545165	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2545167	0.84[GIH][hapmap]
rs2545169	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2546111	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2546116	0.81[EUR][1000 genomes]
rs2909786	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs2909787	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs2909958	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs2952615	1.00[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35130225	0.83[ASN][1000 genomes]
rs351770	0.84[CEU][hapmap]
rs351771	0.94[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs380144	0.81[ASN][1000 genomes]
rs382260	0.84[GIH][hapmap]
rs386830	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs392907	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs395266	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397768	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs401908	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41115	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs411356	0.88[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.81[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs42427	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs429427	0.84[GIH][hapmap]
rs430665	0.84[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap]
rs433429	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs434157	0.85[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs438252	0.81[ASN][1000 genomes]
rs455412	0.91[CEU][hapmap]
rs458451	0.84[CEU][hapmap]
rs458967	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs459552	1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs460832	0.87[CEU][hapmap]
rs461866	0.84[CEU][hapmap]
rs464002	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs464708	0.88[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs465899	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs469727	0.84[CEU][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap]
rs469827	0.84[CEU][hapmap]
rs481789	0.84[EUR][1000 genomes]
rs497844	0.92[CEU][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs529076	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544243	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs563556	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs565453	0.84[EUR][1000 genomes]
rs565603	0.84[EUR][1000 genomes]
rs569940	0.80[AFR][1000 genomes]
rs698405	0.84[CEU][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap]
rs712662	0.84[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap]
rs712665	0.84[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap]
rs818427	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs866006	0.88[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032464	chr5:112076061-112192380	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
2	nsv537862	chr5:112076061-112192380	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs501250	APC	Cis_1M	lymphoblastoid	RTeQTL
rs501250	SRP19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112093400-112183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:112103000-112173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:112118200-112177000	Weak transcription	Colonic Mucosa	Colon
4	chr5:112129000-112157400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr5:112129400-112163800	Weak transcription	Small Intestine	intestine
6	chr5:112129600-112163600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr5:112131800-112157800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:112131800-112164000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr5:112132000-112174000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:112132800-112179800	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:112133600-112160800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:112133600-112161400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:112134000-112162800	Weak transcription	Colon Smooth Muscle	Colon
14	chr5:112136600-112176200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr5:112140400-112183800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr5:112141400-112162400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:112143600-112159800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr5:112144200-112159800	Strong transcription	HSMM	muscle
19	chr5:112145400-112165600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:112145600-112156600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:112146200-112165800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr5:112149000-112163600	Weak transcription	A549	lung
23	chr5:112149400-112176400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr5:112149800-112156400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:112149800-112157800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:112149800-112159400	Strong transcription	Adipose Nuclei	Adipose
27	chr5:112149800-112159800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr5:112149800-112166400	Strong transcription	Fetal Thymus	thymus
29	chr5:112150200-112161200	Strong transcription	Primary B cells from cord blood	blood
30	chr5:112150200-112162000	Strong transcription	Fetal Muscle Trunk	muscle
31	chr5:112150200-112177800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr5:112150400-112166600	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr5:112150800-112156000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr5:112151000-112155800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:112151400-112176400	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr5:112151600-112155800	Strong transcription	Hela-S3	cervix
37	chr5:112152000-112157800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:112152000-112164200	Weak transcription	HMEC	breast
39	chr5:112152000-112170400	Weak transcription	Brain Angular Gyrus	brain
40	chr5:112152000-112183800	Weak transcription	Gastric	stomach
41	chr5:112152200-112156600	Weak transcription	Lung	lung
42	chr5:112152200-112163600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr5:112152200-112172000	Weak transcription	NHLF	lung
44	chr5:112153200-112156800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr5:112153200-112159200	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr5:112153200-112159400	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr5:112153200-112160000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:112153200-112169600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr5:112153200-112179400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:112153200-112179800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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